# Navigating mass spectral similarity in high-resolution MS/MS metabolomics data

## Documentation for package ‘MetCirc’ version 1.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

adduct | 'adduct' returns adduct ion names of compounds in 'MSP'-object
adduct-method | 'adduct' returns adduct ion names of compounds in 'MSP'-object
adduct<- | 'adduct<-' sets adduct ion names in 'MSP'-object
adduct<--method | 'adduct<-' sets adduct ion names in 'MSP'-object
allocatePrecursor2mz | allocatePrecursor2mz: Join two data sources
binnedMSP | Example data for 'MetCirc': 'binnedMSP'
binning | Bin m/z values
cart2Polar | Calculate polar coordinates from cartesian coordinates
circosLegend | Plot a legend for circos plot
classes | 'classes' returns class names of compounds in 'MSP'-object
classes-method | 'classes' returns class names of compounds in 'MSP'-object
classes<- | 'classes<-' sets information in 'MSP'-object
classes<--method | 'classes<-' sets information in 'MSP'-object
combine | 'combine' method for 'MSP'-class
combine-method | 'combine' method for 'MSP'-class
compartmentTissue | Example data for 'MetCirc': 'compartmentTissue'
convert2MSP | Convert deconvoluted matrix into 'MSP'-object
convertExampleDF | Example data for 'MetCirc': convertExampleDF
convertMSP2MSP | Convert MSP data frame into object of 'MSP'-class
createLink0Matrix | Create a link matrix
createLinkMatrix | Create a matrix which contains features to link (indices)
createOrderedSimMat | Update colnames and rownames of a similarity matrix according to order m/z, retention time and clustering
createSimilarityMatrix | Create similarity matrix
cutLinkMatrix | Create a cut link matrix
cutUniquePrecursor | Get unique precursor ions
finalMSP | Example data for 'MetCirc': 'finalMSP'
getBegEndIndMSP | Get beginning and end indices of each entry in a 'data.frame' in 'peaks(MSP)'-objects
getLinkMatrixIndices | Get indices in LinkMatrix of feature
getPrecursorMZ | 'getPrecursorMZ' returns precursor m/z values of an 'MSP'-object
getPrecursorMZ-method | 'getPrecursorMZ' returns precursor m/z values of an 'MSP'-object
getRT | 'getRT' returns precursor RT values of an 'MSP'-object
getRT-method | 'getRT' returns precursor RT values of an 'MSP'-object
highlight | Add links and highlight sectors
idMSMStoMSP-data | Example data for 'MetCirc': 'finalMSP'
information | 'information' returns information of metabolites in 'MSP'-object
information-method | 'information' returns information of metabolites in 'MSP'-object
information<- | 'information<-' sets information in 'MSP'-object
information<--method | 'information<-' sets information in 'MSP'-object
length | 'length' method for 'MSP'-class
length-method | 'length' method for 'MSP'-class
minFragCart2Polar | Calculate the nearest feature in polar coordinates given cartesian coordinates
MSP | MSP-class
MSP-class | MSP-class
msp2FunctionalLossesMSP | Convert MSP to MSP with functional losses
msp2msp | Example data for 'MetCirc': 'msp2msp'
names | 'names' returns names in 'MSP'-object
names-method | 'names' returns names in 'MSP'-object
names<- | 'names<-' sets names in 'MSP'-object
names<--method | 'names<-' sets names in 'MSP'-object
NDP | Calculate the normalised dot product
peaks | 'peaks' method for 'MSP'-class
peaks-method | 'peaks' method for 'MSP'-class
plotCircos | Circular plot to visualise similarity
printInformationSelect | Display information on connected features of selected features
sd01_outputXCMS | Example data for 'MetCirc': 'sd01_outputXCMS'
sd02_deconvoluted | Example data for 'MetCirc': sd02_deconvoluted
shinyCircos | Interactive visualisation of similarity and navigation of MS/MS features
show | 'show' method for 'MSP'-class
show-method | 'show' method for 'MSP'-class
similarityMat | Example data for 'MetCirc': 'similarityMat'
thresholdLinkMatrix | Threshold a link matrix
tissue | Example data for 'MetCirc': 'tissue'
truncateName | Truncate names
[ | Extract parts of a 'MSP'-object
[-method | Extract parts of a 'MSP'-object